Search

In order to extract neutrino oscillation parameters, long-baseline neutrino oscillation experiments rely on detailed models of neutrino interactions with nuclei. These models constitute an important source of systematic uncertainty, partially because detectors to date have been blind to final state neutrons. Three-dimensional projection scintillator trackers comprise components of the near detectors of the next generation long-baseline neutrino experiments. Due to the good timing resolution and fine granularity, this technology is capable of measuring neutron kinetic energy in neutrino interactions on an event-by-event basis and will provide valuable data for refining neutrino interaction models and ways to reconstruct neutrino energy. Two prototypes have been exposed to the neutron beamline at Los Alamos National Laboratory (LANL) in both 2019 and 2020, with neutron energies between 0 and 800 MeV. In order to demonstrate the capability of neutron detection, the total neutron-scintillator cross section as a function of neutron energy is measured and compared to external measurements. The measured total neutron cross section in scintillator between 98 and 688 MeV is 0.36 ± 0.05 barn.

Introduction According to current diagnostic systems, affective symptoms do not represent a fundamental criterion for the diagnosis of DD. However, numerous studies have highlighted frequent comorbidity between DD and Mood Disorders and have elucidated the importance of the affective state in the development and persistence of delusions. Thus, some factor analysis studies have identified the existence of a depressive dimension in DD, suggesting a substantial psychopathological heterogeneity in DD. However, these important affective features have not evaluated from a phenomenological point of view and in their relationship with delusions. Objectives The aim of the present study is to investigate the relationship between personality, trait affectivity and severity of delusions in patients with Delusional Disorder (DD). Methods Thirty-two outpatients affected by DD were administered the Structured Interview for DSM-IV-TR Personality Disorders (SIDP-IV), the Pathological Narcissism Inventory (NPI), the Positive and Negative Affect Schedule (PANAS) and the Psychotic Symptom Rating Scale (PSYRATS). Next, we analysed the prevalence of personality disorder in our sample of patients with DD and studied the correlations between the severity of delusions and the different affective variables. Finally, we obtained a multivariate explanatory model of the severity of the delusions. Results The severity of delusions was directly associated with “Grandiose Fantasy” item of narcissistic personality and inversely related with the feelings of shame, fear and guilt. In the multivariate model, the feeling of shame was the only independent variable capable of accounting for the severity of the delusions, that, in in DD patients, would lie on an affective core of shame.Table 2. Pearson correlation coefficient VARIABLES DRS total score GRANDIOSE FANTASY p = 0.045 SHAME p = 0.048 GUILT p = 0.016 AGITATION p = 0.049 FEAR p = 0.041 Table 3. Standardized coefficients in linear standard regression (DRS) DRS: total score R² β t p Step 1 0.157 - - - GRANDIOSE FANTASY - 0.396 1.89 0.048 Step 2 0.460 - - - GRANDIOSE FANTASY - 0.291 1.65 0.116 SHAME - -0.560 -3.17 0.005 Conclusions The severity of delusional beliefs in DD patients would lie on an affective core of shame upon predisposing personality traits. These findings could help to develop a psychotherapeutic approach for delusional patients focused in the feeling of shame. Disclosure of Interest None Declared

Abstract Neurotypical individuals have subjective sensitivity differences that may overlap with more heavily studied clinical populations. However, it is not known whether these subjective differences in sensory sensitivity are modality specific, or lead to behavioral shifts. In our experiment, we measured the oral touch sensitivity and food texture awareness differences in two neurotypical groups having either a high or low subjective sensitivity in touch modality. To measure oral touch sensitivity, individuals performed discrimination tasks across three types of stimuli (liquid, semisolid, and solid). Next, they performed two sorting exercises for two texture-centric food products: cookies and crackers. The stimuli that required low oral processing (liquid) were discriminated at higher rates by participants with high subjective sensitivity. Additionally, discrimination strategies between several foods in the same product space were different across the groups, and each group used attributes other than food texture as differentiating characteristics. The results show subjective touch sensitivity influences behavior (sensitivity and awareness). However, we show that the relationship between subjective touch sensitivity and behavior generalizes beyond just touch to other sensory modalities.

The paper reports the results from the observational retrospective-prospective RUBINO study conducted in Italy to assess the safety of rituximab in the treatment of rheumatoid arthritis (RA) in routine clinical practice. The percentage of patients who manifested at least one grade 3 or 4 adverse event (AE) assessed by the Common Terminology Criteria for Adverse Events version 3.0 (CTCAE v.3) during the observation period (primary objective) was evaluated. The percentage of patients manifesting a severe AE (SAE), clinical response to rituximab treatment, clinical remission according to disease activity score for 28 joints (DAS28) criteria, markers of disease and quality of life were also assessed. Fifty-three Italian rheumatology centers took part in the study. Patients with a diagnosis of RA and inadequate response to anti-tumor necrosis factor b (anti-TNFa) drugs were enrolled. Participating patients had previously received at least one cycle of rituximab, and treatment was still ongoing at the time of recruitment. Out of 205 patients enrolled, 60% manifested no form of AE, 14.2% had at least one grade 3 or 4 AE, and 11.2% patients reported an SAE. The overall percentage of patients manifesting AEs (40%) was lower compared to the DANCER (81% and 85%), REFLEX (85%) and RESET (85% and 69%) studies, but higher than that observed in the CERERRA registry (from 10.2% to 13.9%). This difference may be due to the shorter observation period applied in the CERERRA registry (only 12 months) compared to the RUBINO study (up to 3 years). All parameters of RA activity (erythrocyte sedimentation rate, C-reactive protein, health assessment questionnaire score, DAS28) improved significantly during the study.

Several studies demonstrated the efficacy of the B-cell depletion therapy with rituximab (RTX) in RA patients, including those unresponsive to anti- TNF therapy, underlying the important role of B cells in this disease (1-5). Several recent papers have demonstrated a differential effects of RTX in depleting B-cells and blocking plasma cell generation at the synovial and at the bone marrow level (7-9). This differential effect may explain why among patients who respond to RTX, some relapse while others show a very prolonged response, independently from the reappearance of B-cells in the peripheral blood (6). However, the efficacy of RTX may also depend on the individual genetic predisposition. At this regard, very few data were produced by now.

Multigene families often play an important role in host-parasite interactions. One of the largest multigene families in Theileria parva, the causative agent of East Coast fever, is the T. parva repeat (Tpr) gene family. The function of the putative Tpr proteins remains unknown. The initial publication of the T. parva reference genome identified 39 Tpr family open reading frames (ORFs) sharing a conserved C-terminal domain. Twenty-eight of these are clustered in a central region of chromosome 3, termed the "Tpr locus", while others are dispersed throughout all four nuclear chromosomes. The Tpr locus contains three of the four assembly gaps remaining in the genome, suggesting the presence of additional, as yet uncharacterized, Tpr gene copies. Here, we describe the use of long-read sequencing to attempt to close the gaps in the reference assembly of T. parva (located among multigene families clusters), characterize the full complement of Tpr family ORFs in the T. parva reference genome, and evaluate their evolutionary relationship with Tpr homologs in other Theileria species. We identify three new Tpr family genes in the T. parva reference genome and show that sequence similarity among paralogs in the Tpr locus is significantly higher than between genes outside the Tpr locus. We also identify sequences homologous to the conserved C-terminal domain in five additional Theileria species. Using these sequences, we show that the evolution of this gene family involves conservation of a few orthologs across species, combined with gene gains/losses, and species-specific expansions., (© 2023. The Author(s).)

The tick-transmitted apicomplexan Theileria parva causes East Coast fever, a bovine disease of great economic and veterinary importance in Africa. Papain-like cysteine proteases play important roles in protozoan parasite host cell entry and egress, nutrition and host immune evasion. This study reports the identification and characterisation of a T. parva strain Muguga cathepsin L-like (C1A subfamily) cysteine protease (ThpCP). Molecular modelling confirmed the papain-like fold of ThpCP, hydrophobic character of the S2 substrate binding pocket and non-covalent interaction between the pro- and catalytic domains preceding low pH autoactivation. ThpCP was recombinantly expressed in a protease deficient E. coli (Rosetta (DE3)pLysS strain) expression host as a 46 kDa proenzyme. Following Ni-chelate affinity chromatography and acidification, the 27 kDa mature ThpCP was purified by cation-exchange chromatography. Purified ThpCP hydrolysed typical cathepsin L substrates N-α-benzyloxycarbonyl (Z)-Phe-Arg-7-amino-4-methyl-coumarin (AMC) (k cat /K m  = 4.49 × 10 5 s -1 M -1 ) and Z-Leu-Arg-AMC (k cat /K m  = 4.20 × 10 5 s -1 M -1 ), but showed no activity against the cathepsin B-selective substrate Z-Arg-Arg-AMC. Recombinant ThpCP was active over a broad pH range from pH 4.5 to 7.5, thereby showing potential activity in the acidic parasite food vacuole and close to neutral pH of the host lymphocyte cytoplasm. Recombinant ThpCP was inhibited by the cysteine protease inhibitors E64, iodoacetate, leupeptin, chymostatin, Z-Phe-Ala-diazomethylketone (DMK) and Z-Phe-Phe-DMK and hydrolysed bovine proteins: haemoglobin, immunoglobulin G, serum albumin and fibrinogen as well as goat IgG at pH 6 and 7. Functional expression and characterisation of Theileria cysteine proteases should enable high throughput screening of cysteine protease inhibitor libraries against these proteases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.)

Antimicrobial resistance (AMR) is a global public health threat for both human and veterinary medicine. Increasing evidence suggests that animals are important sources of AMR to humans; however, most of these studies focus on production animals. In order to determine the pattern of AMR in pets, mainly in dogs in Africa, a meta-analysis was performed with AMR studies conducted in African countries and published between January 2000 and January 2021 in four databases: Medline (PubMed), Scopus, Cab abstract and Google Scholar. Seven bacterial strains, namely Staphylococcus aureus, Escherichia coli, Salmonella spp., Pseudomonas aeruginosa, Streptococcus pyogenes, coagulase-negative Staphylococcus (SNC) and Staphylococcus pseudintermedius were included in this study. A total of 18 out of 234 indexed articles met the study criteria. The results revealed that multiple bacteria were resistant to various commonly used antibiotics including enrofloxacin, ciprofloxacin, gentamicin, amoxicillin, clavulanic acid, cotrimoxazole, streptomycin, tetracycline and chloramphenicol. Concerning multidrug resistance, E. coli strains came first with the highest prevalence of 98%, followed by P. aeroginosa (92%) and Salmonella spp. (53%). In contrast, the overall prevalence of multidrug resistance was low for S. aureus (18%) and S. pseudintermedius (25%). It is therefore urgent to find, as soon as possible, alternatives to replace these antibiotics, which have become ineffective in controlling these bacteria in dogs in Africa. Moreover, further metagenomic studies are needed to describe the full resistome and mobilome in dogs regardless of the bacteria.

Background: African swine fever (ASF) is a lethal hemorrhagic disease affecting domestic pigs resulting in up to 100% mortality rates caused by the ASF virus (ASFV). The locally-adapted pigs in South-western Kenya have been reported to be resilient to disease and harsh climatic conditions and tolerate ASF; however, the mechanisms by which this tolerance is sustained remain largely unknown. We evaluated the gene expression patterns in spleen tissues of these locally-adapted pigs in response to varying infective doses of ASFV to elucidate the virus-host interaction dynamics., Methods: Locally adapted pigs (n = 14) were experimentally infected with a high dose (1x10 6 HAD 50 ), medium dose (1x10 4 HAD 50 ), and low dose (1x10 2 HAD 50 ) of the highly virulent genotype IX ASFV Ken12/busia.1 (Ken-1033) isolate diluted in PBS and followed through the course of infection for 29 days. The in vivo pig host and ASFV pathogen gene expression in spleen tissues from 10 pigs (including three from each infective group and one uninfected control) were analyzed in a dual-RNASeq fashion. We compared gene expression between three varying doses in the host and pathogen by contrasting experiment groups against the naïve control., Results: A total of 4954 differentially expressed genes (DEGs) were detected after ASFV Ken12/1 infection, including 3055, 1771, and 128 DEGs in the high, medium, and low doses, respectively. Gene ontology and KEGG pathway analysis showed that the DEGs were enriched for genes involved in the innate immune response, inflammatory response, autophagy, and apoptosis in lethal dose groups. The surviving low dose group suppressed genes in pathways of physiopathological importance. We found a strong association between severe ASF pathogenesis in the high and medium dose groups with upregulation of proinflammatory cytokines and immunomodulation of cytokine expression possibly induced by overproduction of prostaglandin E synthase (4-fold; p < 0.05) or through downregulation of expression of M1-activating receptors, signal transductors, and transcription factors. The host-pathogen interaction resulted in induction of expression of immune-suppressive cytokines (IL-27), inactivation of autophagy and apoptosis through up-regulation of NUPR1 [5.7-fold (high dose) and 5.1-fold (medium dose) [p < 0.05] and IL7R expression. We detected repression of genes involved in MHC class II antigen processing and presentation, such as cathepsins, SLA-DQB1, SLA-DOB, SLA-DMB, SLA-DRA, and SLA-DQA in the medium and high dose groups. Additionally, the host-pathogen interaction activated the CD8 + cytotoxicity and neutrophil machinery by increasing the expression of neutrophils/CD8 + T effector cell-recruiting chemokines (CCL2, CXCL2, CXCL10, CCL23, CCL4, CXCL8, and CXCL13) in the lethal high and medium dose groups. The recovered pigs infected with ASFV at a low dose significantly repressed the expression of CXCL10, averting induction of T lymphocyte apoptosis and FUNDC1 that suppressed neutrophilia., Conclusions: We provide the first in vivo gene expression profile data from locally-adapted pigs from south-western Kenya following experimental infection with a highly virulent ASFV genotype IX isolate at varying doses that mimic acute and mild disease. Our study showed that the locally-adapted pigs induced the expression of genes associated with tolerance to infection and repression of genes involved in inflammation at varying levels depending upon the ASFV dose administered., (© 2022. The Author(s).)

Ralstonia solanacearum is a pathogen causing bacterial wilt disease of potato, resulting in 70% potato production losses in Kenya. A study was conducted to determine the diversity of R. solanacearum species complex strains within the main potato-growing regions of Kenya. Potato tubers were collected in different potato-growing regions of Kenya from visibly wilted potato plants as well as samples of tomato, irrigation water, and cultures for pathogen isolation. Genomic DNA was isolated from 135 purified cultures of RSSC isolates and PCR-amplified using multiplex and sequevar primers targeting the endoglucanase ( egl ) partial gene sequences. Pathogenicity tests using R. solanacearum strain (phylotype II sequevar I) were done on the cultivars Kenya Karibu, Shangi, Chulu, Wanjiku, and MoneyMaker. Phylogenetic analysis of the partial egl gene identified two genospecies, R. pseudosolanacearum sp. nov. (1.5%) and R. solanacearum (98.5%). All R. solanacearum strains clustered in sequevar I and were distributed in all the potato-growing regions surveyed. The cultivars were grown in a greenhouse for two cycles in a randomized complete block design and inoculated with R. solanacearum strain. The severity scores were assessed and the area under the disease progress curve (AUDPC) was determined. All the cultivars tested for pathogenicity exhibited wilting symptoms at varying intervals after infection, with none showing complete resistance to R. solanacearum . Cultivar Shangi exhibited minimum disease severity and progression of 41.14% and AUDPC of 1041.7, respectively, while 'Kenya Karibu' was the most susceptible with a high progression rate of 68.24% and AUDPC of 1897.5, respectively. 'MoneyMaker', 'Chulu', and 'Wanjiku' showed no significant difference in disease severity, depicting a simultaneous rate of infection among them. These findings provide valuable information to better understand the pathogen genetic diversity in Kenya and how it spreads.

One of the crucial public health problems today is the emerging and re-emerging of multidrug-resistant (MDR) bacteria coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella (NTS) is classified among the MDR pathogens of international concern. To predict their MDR potentials, 23 assembled genomes of NTS from live cattle (n = 1), beef carcass (n = 19), butchers’ hands (n = 1) and beef processing environments (n = 2) isolated from 830 wet swabs at the Yaounde abattoir between December 2014 and November 2015 were explored using whole-genome sequencing. Phenotypically, while 22% (n = 5) of Salmonella isolates were streptomycin-resistant, 13% (n = 3) were MDR. Genotypically, all the Salmonella isolates possessed high MDR potentials against several classes of antibiotics including critically important drugs (carbapenems, third-generation cephalosporin and fluoroquinolone). Moreover, >31% of NTS exhibited resistance potentials to polymyxin, considered as the last resort drug. Additionally, ≤80% of isolates harbored “silent resistant genes” as a potential reservoir of drug resistance. Our isolates showed a high degree of pathogenicity and possessed key virulence factors to establish infection even in humans. Whole-genome sequencing unveiled both broader antimicrobial resistance (AMR) profiles and inference of pathogen characteristics. This study calls for the prudent use of antibiotics and constant monitoring of AMR of NTS.

This study aimed at assessing haplotype diversity and population dynamics of three Congolese indigenous goat populations that included Kasai goat (KG), small goat (SG), and dwarf goat (DG) of the Democratic Republic of Congo (DRC). The 1169 bp d - loop region of mitochondrial DNA (mtDNA) was sequenced for 339 Congolese indigenous goats. The total length of sequences was used to generate the haplotypes and evaluate their diversities, whereas the hypervariable region (HVI, 453 bp) was analyzed to define the maternal variation and the demographic dynamic. A total of 568 segregating sites that generated 192 haplotypes were observed from the entire d - loop region (1169 bp d - loop ). Phylogenetic analyses using reference haplotypes from the six globally defined goat mtDNA haplogroups showed that all the three Congolese indigenous goat populations studied clustered into the dominant haplogroup A, as revealed by the neighbor-joining (NJ) tree and median-joining (MJ) network. Nine haplotypes were shared between the studied goats and goat populations from Pakistan (1 haplotype), Kenya, Ethiopia and Algeria (1 haplotype), Zimbabwe (1 haplotype), Cameroon (3 haplotypes), and Mozambique (3 haplotypes). The population pairwise analysis ( F ST ) indicated a weak differentiation between the Congolese indigenous goat populations. Negative and significant ( p -value <.05) values for F u's F s (-20.418) and Tajima's (-2.189) tests showed the expansion in the history of the three Congolese indigenous goat populations. These results suggest a weak differentiation and a single maternal origin for the studied goats. This information will contribute to the improvement of the management strategies and long-term conservation of indigenous goats in DRC., Competing Interests: No conflict of interest was reported by the author(s)., (© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Salmonella enteritidis is a major causative agent of foodborne illnesses worldwide. As the traditional serotyping and quantification methods are labor-intensive, time-consuming, and expensive, faster and more convenient molecular diagnostic methods are needed. In this study, we developed and validated a rapid duplex TaqMan real-time polymerase chain reaction (PCR) for the accurate identification and quantification of S. enteritidis. The primers and TaqMan probes were designed based on the S. enteritidis-specific gene lygD and the Salmonella genus-specific gene invA. The melt curve and gel electrophoresis analysis showed that the designed primers had potent specificity for the amplification of lygD and invA. The duplex real-time PCR specifically identified S. enteritidis from a panel of 40 Salmonella strains that represented 29 serovars and 12 non-Salmonella organisms. The duplex real-time PCR assay detected four copies of S. enteritidis DNA per reaction. The intra- and inter- assays indicated a high degree of reproducibility. The real-time PCR could accurately detect and quantify S. enteritidis in chicken organs after Salmonella infection. Furthermore, the assay identified 100% of the S. enteritidis and Salmonella genus isolates from chicken egg samples with superior sensitivity after 6 h of pre-enrichment compared to the traditional culture method. Additionally, the most-probable-number (MPN) combined with qPCR and a shortened incubation time (MPN-qPCR-SIT) method was developed for the population determination of S. enteritidis and compared with various enumeration methods. Thus, we have established and validated a new duplex real-time PCR assay and MPN-qPCR-SIT method for the accurate detection and quantification of S. enteritidis, which could contribute to meeting the need for fast detection and identification in prevention and control measures for food safety.

Tanzania has a goat population of about 24.8 million most of which belong to the Small East African breed distributed in almost all agro-ecological zones. The different goat populations and the production system in which they are raised are not well characterized depriving animal breeders useful information in designing and running improvement and conservation programs. Therefore, the study was conducted in all agro-ecological zones in Tanzania to characterize the indigenous goats and the production system in which they are raised. Data on animals were collected from 688 randomly selected adult female goats and for production system description; 220 households were interviewed. Analysis of variance and discriminant analysis were used on quantitative data, while frequency analysis was used on qualitative data. Income generation and meat production were the primary goat rearing objectives. More than 55% of respondents grazed their animals freely in communal lands where natural pasture was the chief feed resource. Mating was mainly uncontrolled with apron and castration being used by goat keepers as mating control methods. Common diseases were contagious caprine pleural pneumonia and helminthiasis. Feed shortage, prevalence of diseases, and water scarcity were the major goat production constraints. There were morphological variations between and within these goat populations, and based on quantitative data, the goats were categorized into two groups. High twinning was observed in Ujiji and Lindi goats and low for Sukuma. The dominant coat color was plain white in Pare, Gogo, Maasai, and Tanga. Other coat color patterns were mixed black and white for Sukuma, reddish-brown for Lindi, black and reddish-brown for Ujiji, and white and reddish-brown for Pwani and Maasai. High within population variation is observed which is important as it can be used as a basis for genetic improvement through selection., (© 2022. The Author(s).)

The Potyvirus Moroccan watermelon mosaic virus (MWMV) naturally infects and severely threatens production of cucurbits and papaya. In this study, we identified and characterized MWMV isolated from pumpkin ( Cucurbita moschata ) intercropped with MWMV-infected papaya plants through next-generation sequencing (NGS) and Sanger sequencing approaches. Complete MWMV genome sequences were obtained from two pumpkin samples through NGS and validated using Sanger sequencing. The isolates shared 83.4 to 83.7% nucleotide (nt) and 92.3 to 95.1% amino acid (aa) sequence identities in the coat protein and 79.5 to 79.9% nt and 89.2 to 89.7% aa identities in the polyprotein with papaya isolates of MWMV. Phylogenetic analysis using complete polyprotein nt sequences revealed the clustering of both pumpkin isolates of MWMV with corresponding sequences of cucurbit isolates of the virus from other parts of Africa and the Mediterranean regions, distinct from a clade formed by papaya isolates. Through sap inoculation, a pumpkin isolate of MWMV was pathogenic on zucchini ( Cucurbita pepo ), watermelon ( Citrullus lanatus ), and cucumber ( Cucumis sativus ) but not on papaya. Conversely, the papaya isolate of MWMV was nonpathogenic on pumpkin, watermelon, and cucumber, but it infected zucchini. The results suggest the occurrence of two strains of MWMV in Kenya having different biological characteristics associated with the host specificity.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A recent research study on prevalence of tick-borne pathogens in Burundi reported high prevalence and endemicity of Theileria parva, Anaplasma marginale and Babesia bigemina infections in cattle. Detailed information about tick species infesting animals, their distribution and genetic diversity in Burundi is outdated and limited. This study therefore assessed the prevalence and genetic diversity of tick species infesting cattle across agroecological zones (AEZs) in Burundi. A cross-sectional study on the occurrence of tick species was conducted in 24 districts of Burundi between October and December 2017. Differential identification and characterization of ticks collected was conducted using tick morphological keys and molecular tools (cox1 and 12S rRNA gene). Chi-square test was used to test for association between agroecological zones and the prevalence of tick species. Phylogenetic relationships were inferred using bayesian and maximum likelihood algorithms. A total of 483 ticks were collected from the five AEZs sampled. Six tick species comprising of Rhipicephalus appendiculatus, R. sanguineus, R. evertsi evertsi, R. microplus, R. decoloratus and Amblyomma variegatum were observed. Rhipicephalus appendiculatus were the most prevalent ticks (~45%). A total of 138 specimens (28%) were found to be Rhipicephalus microplus, suggesting an emerging threat for cattle farmers. Twelve R. appendiculatus cox1 haplotypes were obtained from 106 specimens that were sequenced. Two cox1 haplotypes of R. microplus which clustered into previously reported Clade A were observed. Rhipicephalus sanguineus and R. evertsi evertsi ticks, the vectors of numerous zoonotic pathogens, were collected from cattle, which constitute a high risk for public health. These findings reveal an overlapping distribution of tick vectors in Burundi. The design of ticks and tick-borne diseases control strategies should consider the distribution of different vectors across the AEZs particularly the presence of the highly invasive R. microplus tick in Burundi and the potential risk of introducing the pathogenic Babesia bovis., Competing Interests: The authors have declared that no competing interests exist.

African swine fever (ASF) is a highly infectious and fatal haemorrhagic disease of pigs that is caused by a complex DNA virus of the genus Asfivirus and Asfarviridae African suids family. The disease is among the most devastating pig diseases worldwide including Africa. Although the disease was first reported in the 19th century, it has continued to spread in Africa and other parts of the world. Globally, the rising demand for pork and concomitant increase in transboundary movements of pigs and pork products is likely to increase the risk of transmission and spread of ASF and pose a major challenge to the pig industry. Different genotypes of the ASF virus (ASFV) with varying virulence have been associated with different outbreaks in several countries in sub-Saharan Africa (SSA) and worldwide, and understanding genotype circulation will be important for ASF prevention and control strategies. ASFV genotypes unique to Africa have also been reported in SSA. This review briefly recounts the biology, genomics and genotyping of ASFV and provides an account of the different genotypes circulating in SSA. The review also highlights prevention, control and progress on vaccine development and identifies gaps in knowledge of ASFV genotype circulation in SSA that need to be addressed.

The Small East African (SEA) goat are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goat populations, namely Fipa, Songwe, Tanga, Pwani, Iringa, Newala, Lindi, Gogo, Pare, Maasai, Sukuma, and Ujiji, based on the mitochondrial DNA (mtDNA) D-loop. High haplotype ( H d = 0.9619-0.9945) and nucleotide ( π = 0.0120-0.0162) diversities were observed from a total of 389 haplotypes. The majority of the haplotypes ( n = 334) belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B, and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country., Competing Interests: There are no conflicts of interest between authors, and permission from each author has been granted., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I ( SLA-1 , SLA-2 ) and II ( DQB1 ) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1 , SLA-2 , and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.

African swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the continent since 1961, there have been no genome-level analyses of virus evolution in Africa. The virus was recently transported from south-eastern Africa to Georgia in 2007 and has subsequently spread to Russia, eastern Europe, China, and south-east Asia with devastating socioeconomic consequences. To date, two of the 24 currently described ASFV genotypes defined by sequencing of the p72 gene, namely genotype I and II, have been reported outside Africa, with genotype II being responsible for the ongoing pig pandemic. Multiple complete genotype II genome sequences have been reported from European, Russian and Chinese virus isolates but no complete genome sequences have yet been reported from Africa. We report herein the complete genome of a Tanzanian genotype II isolate, Tanzania/Rukwa/2017/1, collected in 2017 and determined using an Illumina short read strategy. The Tanzania/Rukwa/2017/1 sequence is 183,186 bp in length (in a single contig) and contains 188 open reading frames. Considering only un-gapped sites in the pairwise alignments, the new sequence has 99.961% identity with the updated Georgia 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16&#95;29413&#95;o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This represents 73 single nucleotide polymorphisms (SNPs) relative to the Polish isolate and 78 SNPs with the Chinese genome. Phylogenetic analysis indicated that Tanzania/Rukwa/2017/1 clusters most closely with Georgia 2007/1. The majority of the differences between Tanzania/Rukwa/2017/1 and Georgia 2007/1 genotype II genomes are insertions/deletions (indels) as is typical for ASFV. The indels included differences in the length and copy number of the terminal multicopy gene families, MGF 360 and 110. The Rukwa2017/1 sequence is the first complete genotype II genome from a precisely mapped locality in Africa, since the exact origin of Georgia2007/1 is unknown. It therefore provides baseline information for future analyses of the diversity and phylogeography of this globally important genetic sub-group of ASF viruses.

β-amylase is a thermostable enzyme that hydrolyses starch during cooking of sweetpotato ( Ipomoea batatas ) storage roots, thereby influencing eating quality. Its activity is known to vary amongst genotypes but the genetic diversity of the beta-amylase gene ( Amyβ ) is not well studied. Amyβ has a highly conserved region between exon V and VI, forming part of the enzyme's active site. To determine the gene diversity, a 2.3 kb fragment, including the conserved region of the Amyβ gene was sequenced from 25 sweetpotato genotypes. The effect of sequence variation on gene expression, enzyme activity, and firmness in cooked roots was determined. Six genotypes carrying several SNPs within exon V, linked with an AT or ATGATA insertion in intron V were unique and clustered together. The genotypes also shared an A336E substitution in the amino acid sequence, eight residues upstream of a substrate-binding Thr344. The genotypes carrying this allele exhibited low gene expression and low enzyme activity. Enzyme activity was negatively correlated with firmness (R = -0.42) in cooked roots. This is the first report of such an allele, associated with low enzyme activity. These results suggest that genetic variation within the AmyB locus can be utilized to develop markers for firmness in sweetpotato breeding., Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results., (© 2021 The Author(s).)

Brucellosis, caused by several species of the genus Brucella, is a zoonotic disease that affects humans and animal species worldwide. Information on the Brucella species circulating in different hosts in Kenya is largely unknown, thus limiting the adoption of targeted control strategies. This study was conducted in multi-host livestock populations in Kenya to detect the circulating Brucella species and assess evidence of host-pathogen associations. Serum samples were collected from 228 cattle, 162 goats, 158 sheep, 49 camels, and 257 humans from Narok and Marsabit counties in Kenya. Information on age, location and history of abortion or retained placenta were obtained for sampled livestock. Data on age, gender and location of residence were also collected for human participants. All samples were tested using genus level real-time PCR assays with primers specific for IS711 and bcsp31 targets for the detection of Brucella. All genus positive samples (positive for both targets) were further tested with a speciation assay for AlkB and BMEI1162 targets, specific for B. abortus and B. melitensis, respectively. Samples with adequate quantities aggregating to 577 were also tested with the Rose Bengal Test (RBT). A total of 199 (33.3%) livestock and 99 (38.5%) human samples tested positive for genus Brucella. Animal Brucella PCR positive status was positively predicted by RBT positive results (OR = 8.3, 95% CI 4.0-17.1). Humans aged 21-40 years had higher odds (OR = 2.8, 95% CI 1.2-6.6) of being Brucella PCR positive compared to the other age categories. The data on detection of different Brucella species indicates that B. abortus was detected more often in cattle (OR = 2.3, 95% CI 1.1-4.6) and camels (OR = 2.9, 95% CI 1.3-6.3), while B. melitensis was detected more in sheep (OR = 3.6, 95% CI 2.0-6.7) and goats (OR = 1.7, 95% CI 1.0-3.1). Both B. abortus and B. melitensis DNA were detected in humans and in multiple livestock host species, suggesting cross-transmission of these species among the different hosts. The detection of these two zoonotic Brucella species in humans further underpins the importance of One Health prevention strategies that target multiple host species, especially in the multi-host livestock populations.

African swine fever (ASF) is a severe haemorrhagic disease of domestic pigs caused by ASF virus (ASFV). ASFV is transmitted by soft ticks (Ornithodoros moubata complex group) and by direct transmission. In Africa, ASF is maintained in transmission cycles of asymptomatic infection involving wild suids, mainly warthogs (Phacochoerus africanus). ASF outbreaks have been reported in many parts of Tanzania; however, active surveillance has been limited to pig farms in a few geographical locations. There is an information gap on whether and where the sylvatic cycle may occur independently of domestic pigs. To explore the existence of a sylvatic cycle in Saadani National Park in Tanzania, blood and serum samples were collected from 19 warthogs selected using convenience sampling along vehicle-accessible transects within the national park. The ticks were sampled from warthog burrows. Blood samples and ticks were subjected to ASFV molecular diagnosis (PCR) and genotyping, and warthog sera were subjected to serological (indirect ELISA) testing for ASFV antibody detection. All warthog blood samples were PCR-negative, but 16/19 (84%) of the warthog sera were seropositive by ELISA confirming exposure of warthogs to ASFV. Of the ticks sampled, 20/111 (18%) were positive for ASFV by conventional PCR. Sequencing of the p72 virus gene fragments showed that ASF viruses detected in ticks belonged to genotype XV. The results confirm the existence of a sylvatic cycle of ASFV in Saadani National Park, Tanzania, that involves ticks and warthogs independent of domestic pigs. Our findings suggest that genotype XV previously reported in 2008 in Tanzania is likely to be widely distributed and involved in both wild and domestic infection cycles. Whole-genome sequencing and analysis of the ASFV genotype XV circulating in Tanzania is recommended to determine the phylogeny of the viruses., (© 2020 The Authors. Transboundary and Emerging Diseases published by Wiley-VCH GmbH.)

Background: African swine fever (ASF), a highly contagious hemorrhagic disease, affects domestic pigs in the Democratic Republic of Congo (DRC) where regular outbreaks are reported leading to high mortality rates approaching 100% in the affected regions. No study on the characteristics of the complete genome of strains responsible for ASF outbreaks in the South Kivu province of DRC is available, limited a better understanding of molecular evolution and spread of this virus within the country. The present study aimed at determining the complete genome sequence of ASFV strains genotype X involved in 2018-2019 ASF disease outbreaks in South Kivu province of DRC., Materials and Methods: Genomic DNA of a spleen sample from an ASFV genotype X-positive domestic pig in Uvira, during the 2018-2019 outbreaks in South Kivu, was sequenced using the Illumina HiSeq X platform. Obtained trimmed reads using Geneious Prime 2020.0.4 were blasted against a pig reference genome then contigs were generated from the unmapped reads enriched in ASFV DNA using Spades implemented in Geneious 2020.0.4. The assembly of the complete genome sequence of ASFV was achieved from the longest overlapping contigs. The new genome was annotated with the genome annotation transfer utility (GATU) software and the CLC Genomics Workbench 8 software was further used to search for any ORFs that failed to be identified by GATU. Subsequent analyses of the newly determined Uvira ASFV genotype X genome were done using BLAST for databases search, CLUSTAL W for multiple sequences alignments and MEGA X for phylogeny., Results: 42 Gbp paired-end reads of 150 bp long were obtained containing about 0.1% of ASFV DNA. The assembled Uvira ASFV genome, termed Uvira B53, was 180,916 bp long that could be assembled in 2 contigs. The Uvira B53genome had a GC content of 38.5%, encoded 168 open reading frames (ORFs) and had 98.8% nucleotide identity with the reference ASFV genotype X Kenya 1950. The phylogenetic relationship with selected representative genomes clustered the Uvira B53 strain together with ASFV genotype X reported to date (Kenya 1950 and Ken05/Tk1). Multiple genome sequences comparison with the two reference ASFV genotype X strains showed that 130 of the 168 ORFs were fully conserved in the Uvira B53. The other 38 ORFs were divergent mainly due to SNPs and indels (deletions and insertions). Most of 46 multigene family (MGF) genes identified were affected by various genetic variations. However, 8 MGF ORFs present in Kenya 1950 and Ken05/Tk1 were absent from the Uvira B53 genome including three members of MGF 360, four of MGF 110 and one of MGF 100 while one MGF ORF (MGF 360-1L) at the left end of the genome was truncated in Uvira B53. Moreover, ORFs DP96R and p285L were also absent in the Uvira B53 genome. In contrast, the ORF MGF 110-5L present in Uvira B53 and Ken05/Tk1 was missing in Kenya 1950. The analysis of the intergenic region between the I73R and I329L genes also revealed sequence variations between the three genotype X strains mainly characterized by a deletion of 69 bp in Uvira B53 and 36 bp in Kenya 1950, compared to Ken05/Tk1. Assessment of the CD2v (EP402R) antigen unveiled the presence of SNPs and indels particularly in the PPPKPY tandem repeat region between selected variants representing the eight serogroups reported to date. Uvira B53 had identical CD2v variable region to the Uganda (KM609361) strain, the only other ASFV serogroup 7 reported to date., Conclusion: We report the first complete genome sequence of an African swine fever virus (ASFV) p72 genotype X and CD2v serogroup 7, termed Uvira B53. This study provides additional insights on genetic characteristics and evolution of ASFV useful for tracing the geographical spread of ASF and essential for improved design of control and management strategies against ASF.

Background: Tick-borne diseases (TBDs) constitute a major constraint for livestock development in sub-Saharan Africa, with East Coast fever (ECF) being the most devastating TBD of cattle. However, in Burundi, detailed information is lacking on the current prevalence of TBDs and on the associated economic losses from mortality and morbidity in cattle as well as the costs associated with TBD control and treatment. The aim of this study was, therefore, to assess the prevalence and spatial distribution of tick-borne pathogens (TBPs) in cattle across the major agro-ecological zones (AEZs) in Burundi., Methods: In a cross-sectional study conducted in ten communes spanning the five main AEZs in Burundi, blood samples were taken from 828 cattle from 305 farms between October and December 2017. Evidence of Theileria parva infection was assessed by antibody level, measured using a polymorphic immunodominant molecule (PIM) antigen-based enzyme-linked immunosorbent assay (ELISA) and by a T. parva-specific p104 gene-based nested PCR. Antibodies against Theileria mutans infection were detected using the 32-kDa antigen-based indirect ELISA, while the 200-kDa antigen and the major surface protein 5 (MSP5)-based indirect ELISA were used to detect antibodies against Babesia bigemina and Anaplasma marginale, respectively., Results: The prevalence of T. parva across the ten communes sampled ranged from 77.5 to 93.1% and from 67.8 to 90.0% based on the ELISA and PCR analysis, respectively. A statistically significant difference in infection was observed between calves and adult cattle; however, T. parva infection levels were not significantly associated with sex and breed. The seroprevalence indicating exposure to T. mutans, B. bigemina and A. marginale ranged from 30 to 92.1%, 33.7 to 90% and 50 to 96.2%, respectively. Mixed infections of TBPs were detected in 82.91% of cattle sampled, with 11 different combinations of pathogen species detected ., Conclusions: The findings indicate that T. parva, A. marginale and B. bigemina infections are endemic in Burundi. Knowledge of the spatial distribution of TBPs will facilitate the design of effective targeted strategies to control these diseases. There is a need for further investigations of the distribution of tick vectors and the population structure of TBPs in order to identify the key epidemiological factors contributing to TBD outbreaks in Burundi.

The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production., Competing Interests: The authors have declared that no competing interests exist.

Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus . Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

Theileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle- and buffalo-associated T. parva populations. Here, we describe a capture-based target enrichment approach that enables, for the first time, de novo assembly of nearly complete T. parva genomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle- and buffalo-derived T. parva parasites. De novo genome assemblies generated for cattle genotypes differ from the reference by ~54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derived T. parva genome, which is ~20 kb larger than the genome from the reference, cattle-derived, Muguga strain, and contains 25 new potential genes. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derived T. parva and the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an average Wright's fixation index (FST), genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle- and buffalo-derived T. parva parasites more commonly seen between, rather than within, species. These findings present clear implications for vaccine development, further demonstrated by the ability to assemble nearly all known antigens in the buffalo-derived strain, which will be critical in design of next generation vaccines. The DNA capture approach used provides a clear advantage in specificity over alternative T. parva DNA enrichment methods used previously, such as those that utilize schizont purification, is less labor intensive, and enables in-depth comparative genomics in this apicomplexan parasite., Competing Interests: The authors have declared that no competing interests exist.

Background: African swine fever (ASF) is a highly contagious and severe hemorrhagic viral disease of domestic pigs. The analysis of variable regions of African swine fever virus (ASFV) genome led to more genotypic and serotypic information about circulating strains. The present study aimed at investigating the genetic diversity of ASFV strains in symptomatic pigs in South Kivu province of the Democratic Republic of Congo (DRC)., Materials and Methods: Blood samples collected from 391 ASF symptomatic domestic pigs in 6 of 8 districts in South Kivu were screened for the presence of ASFV, using a VP73 gene-specific polymerase chain reaction (PCR) with the universal primer set PPA1-PPA2. To genotype the strains, we sequenced and compared the nucleotide sequences of PPA-positive samples at three loci: the C-terminus of B646L gene encoding the p72 protein, the E183L gene encoding the p54 protein, and the central hypervariable region (CVR) of the B602L gene encoding the J9L protein. In addition, to serotype and discriminate between closely related strains, the EP402L (CD2v) gene and the intergenic region between the I73R and I329L genes were analyzed., Results: ASFV was confirmed in 26 of 391 pigs tested. However, only 19 and 15 PPA-positive samples, respectively, were successfully sequenced and phylogenetically analyzed for p72 (B646L) and p54 (E183L). All the ASFV studied were of genotype X. The CVR tetrameric repeat clustered the ASFV strains in two subgroups: the Uvira subgroup (10 TRS repeats, AAAABNAABA) and another subgroup from all other strains (8 TRS repeats, AABNAABA). The phylogenetic analysis of the EP402L gene clustered all the strains into CD2v serogroup 7. Analyzing the intergenic region between I73R and I329L genes revealed that the strains were identical but contained a deletion of a 33-nucleotide internal repeat sequence compared to ASFV strain Kenya 1950., Conclusion: ASFV genotype X and serogroup 7 was identified in the ASF disease outbreaks in South Kivu province of DRC in 2018-2019. This represents the first report of ASFV genotype X in DRC. CVR tetrameric repeat sequences clustered the ASFV strains studied in two subgroups. Our finding emphasizes the need for improved coordination of the control of ASF.

Background: Mycoplasma mycoides subsp. mycoides (Mmm) is the causative agent of contagious bovine pleuropneumonia in cattle. A prototype subunit vaccine is being developed, however, there is currently no diagnostic test that can differentiate between infected cattle and those vaccinated with the prototype subunit vaccine. This study characterized Mmm proteins to identify potential antigens for use in differentiating infected from vaccinated animals., Results: Ten Mmm antigens expressed as recombinant proteins were tested in an indirect ELISA using experimental sera from control groups, infected, and vaccinated animals. Data were imported into R software for analysis and drawing of the box and scatter plots while Cohen's Kappa assessed the level of agreement between the Mmm antigens. Two vaccine antigens (MSC&#95;0499 and MSC&#95;0776) were superior in detecting antibodies in sera of animals vaccinated with the subunit vaccines while two non-vaccine antigens (MSC&#95;0636 and LppB) detected antibodies in sera of infected animals showing all clinical stages of the disease. Sensitivity and specificity of above 87.5% were achieved when the MSC&#95;0499 and MSC&#95;0636 antigens were tested on sera from vaccinated and infected animals., Conclusions: The MSC&#95;0499 and MSC&#95;0776 antigens were the most promising for detecting vaccinated animals, while MSC&#95;0636 and LppB were the best targets to identify infected animals. Further testing of sera from vaccinated and infected animals collected at different time intervals in the field should help establish how useful a diagnostic test based on a cocktail of these proteins would be.

Theileria parva is a protozoan parasite that causes East Coast fever (ECF), an economically important disease of cattle in Africa. It is transmitted mainly by the tick Rhipicephalus appendiculatus . Research efforts to develop a subunit vaccine based on parasite neutralizing antibodies and cytotoxic T-lymphocytes have met with limited success. The molecular mechanisms underlying T. parva life cycle stages in the tick vector and bovine host are poorly understood, thus limiting progress toward an effective and efficient control of ECF. Transcriptomics has been used to identify candidate vaccine antigens or markers associated with virulence and disease pathology. Therefore, characterization of gene expression throughout the parasite's life cycle should shed light on host-pathogen interactions in ECF and identify genes underlying differences in parasite stages as well as potential, novel therapeutic targets. Recently, the first gene expression profiling of T. parva was conducted for the sporoblast, sporozoite, and schizont stages. The sporozoite is infective to cattle, whereas the schizont is the major pathogenic form of the parasite. The schizont can differentiate into piroplasm, which is infective to the tick vector. The present study was designed to extend the T. parva gene expression profiling to the piroplasm stage with reference to the schizont. Pairwise comparison revealed that 3,279 of a possible 4,084 protein coding genes were differentially expressed, with 1,623 (49%) genes upregulated and 1,656 (51%) downregulated in the piroplasm relative to the schizont. In addition, over 200 genes were stage-specific. In general, there were more molecular functions, biological processes, subcellular localizations, and pathways significantly enriched in the piroplasm than in the schizont. Using known antigens as benchmarks, we identified several new potential vaccine antigens, including TP04&#95;0076 and TP04&#95;0640, which were highly immunogenic in naturally T. parva -infected cattle. All the candidate vaccine antigens identified have yet to be investigated for their capacity to induce protective immune response against ECF., (Copyright © 2020 Atchou, Ongus, Machuka, Juma, Tiambo, Djikeng, Silva and Pelle.)

Background: Brucellosis is an emerging yet neglected zoonosis that has been reported in Kenya. Epidemiological data on brucellosis in ruminants is readily accessible; however, reports on brucellosis in pigs remain limited. This study sought to detect Brucella infection in pig serum by both serological and molecular techniques. Serum from 700 pigs randomly collected at a centralized abattoir in Nairobi region, Kenya were screened in parallel, using both Rose Bengal Test (RBT) and competitive Enzyme-Linked Immuno-sorbent Assay (cELISA) for antibodies against Brucella spp. All sera positive by RBT and 16 randomly selected negative samples were further tested using conventional PCR targeting bcsp31 gene and real-time PCR (RT-PCR) assays targeting IS711 and bcsp31 genes., Results: A prevalence of 0.57% (n = 4/700) was estimated using RBT; none of these samples was positive on cELISA. All RBT positive sera were also positive by both PCRs, while two sero-negative samples also tested positive on RT-PCR (n = 6/20). Brucella abortus was detected in four out of the six PCR positive samples through a real-time multiplex PCR., Conclusion: The detection of antibodies against Brucella spp. and DNA in serum from slaughterhouse pigs confirm the presence of Brucella in pigs. Therefore, investigation of the epidemiology and role of pigs in the transmission of brucellosis in Kenya is needed. Further targeted studies would be useful to systematically quantify and identify the spp. of Brucella in pigs.

Despite the amount of resources deployed and the technological advancements in molecular biology, vaccinology, immunology, genetics, and biotechnology, there are still no effective vaccines against malaria. Immunity to malaria is usually seen to be species- and/or strain-specific. However, there is a growing body of evidence suggesting the possibility of the existence of cross-strain, cross-species, and cross-genus immune responses in apicomplexans. The principle of gene conservation indicates that homologues play a similar role in closely related organisms. The homologue of UB05 in Theileria parva is TpUB05 (XP&#95;763711.1), which has been tested and shown to be associated with protective immunity in East Coast fever. In a bid to identify potent markers of protective immunity to aid malaria vaccine development, TpUB05 was tested in malaria caused by Plasmodium falciparum . It was observed that TpUB05 was better at detecting antigen-specific antibodies in plasma compared to UB05 when tested by ELISA. The total IgG raised against TpUB05 was able to block parasitic growth in vitro more effectively than that raised against UB05. However, there was no significant difference between the two study antigens in recalling peripheral blood mononuclear cell (PBMC) memory through IFN-γ production. This study suggests, for the first time, that TpUB05 from T. parva cross-reacts with UB05 from P. falciparum and is a marker of protective immunity in malaria. Hence, TpUB05 should be considered for possible development as a potential subunit vaccine candidate against malaria.

Newcastle disease (ND) control by vaccination and an institution of biosecurity measures is less feasible in backyard chicken in developing countries. Therefore, an alternative disease control strategy like the genetic selection of less susceptible chicken genotypes is a promising option. In the present study, genetic polymorphism of LEIO258 marker and association with susceptibility to virulent Newcastle disease virus (NDV) infection in Kuroilers, Sasso, and local Tanzanian chicken embryos were investigated. Samples from high (15%) and less (15%) susceptible cohorts were genotyped by sequencing of LEI0258 marker. A total of 75 DNA sequences comprised of 29 Kuroiler, 29 local Tanzanian chickens, and 17 Sasso were analyzed. Neighbor-joining phylogenetic trees were constructed to depict the clustering of LEI0258 marker alleles and relationship with susceptibility. Alleles with frequency ≥3 were considered for association with susceptibility by the use of the inference technique. The present findings suggest that some LEI0258 marker genetic polymorphisms apart from LEI0258 marker allelic based on sizes may be linked with chicken MHC-B haplotypes that confer chickens variability in resistance or susceptibility to infections. Furthermore, these results demonstrate the presence of relationship between LEI0258 marker polymorphisms and variations in chicken susceptibility to NDV infection, which could be utilized in breeding programs designed to improve chicken disease resistance., Competing Interests: The authors declare that there are no conflicts of interest., (Copyright © 2020 Fulgence Ntangere Mpenda et al.)

Background: The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parva. Over a million bovines die each year of ECF, with a tremendous economic burden to pastoralists in endemic countries. Comprehensive, accurate parasite genome annotation can facilitate the discovery of novel chemotherapeutic targets for disease treatment, as well as elucidate the biology of the parasite. However, genome annotation remains a significant challenge because of limitations in the quality and quantity of the data being used to inform the location and function of protein-coding genes and, when RNA data are used, the underlying biological complexity of the processes involved in gene expression. Here, we apply our recently published RNAseq dataset derived from the schizont life-cycle stage of T. parva to update structural and functional gene annotations across the entire nuclear genome., Results: The re-annotation effort lead to evidence-supported updates in over half of all protein-coding sequence (CDS) predictions, including exon changes, gene merges and gene splitting, an increase in average CDS length of approximately 50 base pairs, and the identification of 128 new genes. Among the new genes identified were those involved in N-glycosylation, a process previously thought not to exist in this organism and a potentially new chemotherapeutic target pathway for treating ECF. Alternatively-spliced genes were identified, and antisense and multi-gene family transcription were extensively characterized., Conclusions: The process of re-annotation led to novel insights into the organization and expression profiles of protein-coding sequences in this parasite, and uncovered a minimal N-glycosylation pathway that changes our current understanding of the evolution of this post-translational modification in apicomplexan parasites.

Carica papaya L. is an important fruit crop grown by small- and large-scale farmers in Kenya for local and export markets. However, its production is constrained by papaya ringspot disease (PRSD). The disease is believed to be caused by papaya ringspot virus (PRSV). Previous attempts to detect PRSV in papaya plants showing PRSD symptoms, using enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) procedures with primers specific to PRSV, have not yielded conclusive results. Therefore, the nature of viruses responsible for PRSD was elucidated in papaya leaves collected from 22 counties through Illumina MiSeq next-generation sequencing (NGS) and validated by RT-PCR and Sanger sequencing. Viruses were detected in 38 out of the 48 leaf samples sequenced. Sequence analysis revealed the presence of four viruses: a Potyvirus named Moroccan watermelon mosaic virus (MWMV) and three viruses belonging to the genus Carlavirus. The Carlaviruses include cowpea mild mottle virus (CpMMV) and two putative Carlaviruses -closely related but distinct from cucumber vein-clearing virus (CuVCV) with amino acid and nucleotide sequence identities of 75.7-78.1 and 63.6-67.6%, respectively, in the coat protein genes. In reference to typical symptoms observed in the infected plants, the two putative Carlaviruses were named papaya mottle-associated virus (PaMV) and papaya mild mottle-associated virus (PaMMV). Surprisingly, and in contrast to previous studies conducted in other parts of world, PRSV was not detected. The majority of the viruses were detected as single viral infections, while a few were found to be infecting alongside another virus (for example, MWMV and PaMV). Furthermore, the NGS and RT-PCR analysis identified MWMV as being strongly associated with ringspot symptoms in infected papaya fruits. This study has provided the first complete genome sequences of these viruses isolated from papaya in Kenya, together with primers for their detection-thus proving to be an important step towards the design of long-term, sustainable disease management strategies., (Copyright © 2020 Mumo, Mamati, Ateka, Rimberia, Asudi, Boykin, Machuka, Njuguna, Pelle and Stomeo.)

A major risk factor for the spread of livestock diseases and their vectors is the uncontrolled transboundary movement of live animals for trade and grazing. Such movements constrain effective control of tick-transmitted pathogens, including Theileria parva. Only limited studies have been undertaken to identify ticks and tick-borne diseases (TTBDs) affecting cattle in central African countries, including Cameroon. We hereby report the collection of baseline data on the prevalence of T. parva in Cameroon through a countrywide cross-sectional survey, conducted in 2016, involving collection of blood samples from cattle from 63 sites across the five agro-ecological zones (AEZs) of the country. ELISA-based surveillance of infected cattle was performed on 479 randomly selected samples and revealed specific antibodies to T. parva in 22.7% and T. mutans in 41.1% of cattle. Screening of 1,340 representative DNA samples for the presence of T. parva identified 25 (1.86%) positives using a p104 antigen gene-based nested PCR assay. The positives were distributed across agro-ecological zones I, II, III and V. None of the p104 positive cattle exhibited clinical symptoms of East Coast fever (ECF). Using reverse line blot (RLB), 58 (4.3%) and 1,139 (85%) of the samples reacted with the T. parva and T. mutans oligonucleotide probes, respectively. This represents the first report of T. parva from Cameroon. Surprisingly, no Rhipicephalus appendiculatus ticks, the main vector of T. parva, were identified in a parallel study involving comprehensive morphological and molecular survey of tick species present in the country. Only two of the 25 p104 positive cattle were PCR-positive for the CD8+ T-cell target schizont-expressed antigen gene Tp1. Cloning and sequencing of Tp1 amplicons revealed sequence identity with the reference T. parva Muguga. This new finding raises serious concerns of a potential spread of ECF into the central African region., (© 2020 Blackwell Verlag GmbH.)

Background: Previous studies in the Central African Republic (CAR) have reported the presence of hepatitis B virus (HBV) recombinant genotype E/D and a suspicion of immune escape mutants (IEMs), without further investigation into their impact on prevention and diagnosis. Consequently, this study investigated HBV mutations among hepatitis B surface antigen (HBsAg)-positive patients attending Institut Pasteur de Bangui in the CAR., Methods: Sera from a total of 118 HBsAg-positive patients with no previous history of HBV treatment or vaccination at the Institut Pasteur de Bangui, were sampled between 2017 and 2019. Subsequently, the region spanning the surface and polymerase genes of HBV was amplified by PCR and sequenced. HBV sequences were genotyped/subgenotyped by phylogenetic analysis and serotyped based on predicted amino acid residues at positions s122, s127, s140, s159, and s160. They were then analyzed for HBV IEMs and polymerase mutations., Results: The region spanning the surface and polymerase genes was successfully amplified and sequenced for 51 samples. Of the HBV sequences, 49 were genotype E and two were genotype A subgenotype A1; these were serotyped as ayw4 and ayw1, respectively. Potential IEMs sY100C, sA128V, and sM133T, and several polymerase mutants were identified., Conclusions: This study raises awareness of the need for further studies to be conducted on a large scale to better understand HBV mutations for improved disease control and prevention strategies in the country., (Copyright © 2019 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

African swine fever (ASF) is the most important disease constraining smallholder pig production in the Democratic Republic of Congo, causing high mortality in domestic pigs with severe impacts on the livelihoods of local populations. This study was conducted with the aim of determining the prevalence of ASF and circulating virus genotypes in asymptomatic pigs raised on smallholder farms in the South Kivu province to understand the transmission dynamics of ASF and ultimately improving disease control. A cross-sectional survey was carried out in 5 districts where 267 pig blood were screened for both antibody and viral genome using indirect Enzyme Linked Immunosorbent Assay (ELISA) and polymerase chain reaction (PCR) respectively. Additionally, amplicons from PCR positive samples were sequenced by Sanger method for genetic analysis of ASF virus (ASFV) based on the C-terminal region of the B646L gene that encodes the major capsid protein p72 and the gene E183L encoding the p54 protein. The overall seroprevalence obtained based on antibody to p30 protein was 37 % and was significantly higher (P < 0.05) in adult (>1 year) animals (44.7 %) than in younger (<1 year) ones (33.5 %). Moreover, the seropositivity varied significantly (P < 0.05) according to the pig husbandry system practiced within the districts investigated with Uvira (55 %) and Mwenga (42.2 %) having the highest ASFV antibodies, while the lowest (10.5 %) were in Kalehe. Free-range pigs exhibited a higher level of seropositivity to ASFV antibody (68.9 %) than pigs kept in the pigsty housing system (21.6 %). However, no statistically significant differences (P > 0.05) were observed when sex of the animal and breed were factored. PCR detection of ASFV amplified a specific band of expected size (257 bp) in 61 out of 267 blood samples, confirming the presence of the viral DNA in 22.8 % of asymptomatic domestic pigs. Statistical analysis revealed that ASFV infection in domestic pigs varied significantly (p < 0.001) according to geographical location and breed, with the highest infection rate found in Walungu district (33.7 %) while the lowest was registered in Kalehe (15.8 %). Local pigs (27.2 %) were more infected than crosses (9.2 %). Phylogenetic analyses based on partial sequences of the p72 and p54 genes revealed that all the ASFV detected belonged to genotype IX, which has previously been reported in other parts of DR Congo, and was clustered together with isolates from Kenya, Uganda and Republic of Congo. This study avails the first evidence of the presence of ASF virus in domestic pigs in the absence of outbreaks in South Kivu province, eastern DR Congo, indicating a need to raise awareness among pig farmers and veterinary authorities on the application of biosecurity measures and good husbandry practices to control the disease., (Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Ticks and tick-borne diseases are a major impediment to livestock production worldwide. Cattle trade and transnational transhumance create risks for the spread of ticks and tick-borne diseases and threaten cattle production in the absence of an effective tick control program. Few studies have been undertaken on cattle ticks in the Central African region; therefore, the need to assess the occurrence and the spatial distribution of tick vectors with the aim of establishing a baseline for monitoring future spread of tick borne-diseases in the region is urgent., Results: A total of 7091 ixodid ticks were collected during a countrywide cross-sectional field survey and identified using morphological criteria. Of these, 4210 (59.4%) ticks were Amblyomma variegatum, 1112 (15.6%) Rhipicephalus (Boophilus) microplus, 708 (10.0%) Rhipicephalus (Boophilus) decoloratus, 28 (0.4%) Rhipicephalus (Boophilus) annulatus, 210 (3.0%) Hyalomma rufipes, 768 (10.8%) Hyalomma truncatum, and 19 (0.3%) Rhipicephalus sanguineus. Three ticks of the genus Hyalomma spp. and 33 of the genus Rhipicephalus spp. were not identified to the species level. Cytochrome c oxidase subunit 1 (cox1) gene sequencing supported the data from morphological examination and led to identification of three additional species, namely Hyalomma dromedarii, Rhipicephalus sulcatus and Rhipicephalus pusillus. The finding of the invasive tick species R. microplus in such large numbers and the apparent displacement of the indigenous R. decoloratus is highly significant since R. microplus is a highly efficient vector of Babesia bovis., Conclusions: This study reports the occurrence and current geographical distribution of important tick vectors associated with cattle in Cameroon. It appears that R. microplus is now well established and may be displacing native Rhipicephalus (Boophilus) species, such as R. decoloratus. This calls for an urgent response to safeguard the livestock sector in western central Africa.